Julius Muller
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/TransView |
| Branch: RELEASE_3_11 |
| Last Commit: 1d616da |
| Last Changed Date: 2020-04-27 14:31:44 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:57 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE TransView PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1826/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TransView 1.32.0 Julius Muller
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: TransView |
| Version: 1.32.0 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/TransView_1.32.0.tar.gz && rm -rf TransView.buildbin-libdir && mkdir TransView.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TransView.buildbin-libdir TransView_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL TransView_1.32.0.zip && rm TransView_1.32.0.tar.gz TransView_1.32.0.zip |
| StartedAt: 2020-10-16 18:13:17 -0400 (Fri, 16 Oct 2020) |
| EndedAt: 2020-10-16 18:14:26 -0400 (Fri, 16 Oct 2020) |
| EllapsedTime: 69.5 seconds |
| RetCode: 0 |
| Status: OK |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/TransView_1.32.0.tar.gz && rm -rf TransView.buildbin-libdir && mkdir TransView.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TransView.buildbin-libdir TransView_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL TransView_1.32.0.zip && rm TransView_1.32.0.tar.gz TransView_1.32.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 980k 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 980k 100 980k 0 0 5972k 0 --:--:-- --:--:-- --:--:-- 6203k
install for i386
* installing *source* package 'TransView' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_TransView.c -o R_init_TransView.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bam_plbuf.c -o bam_plbuf.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bin_density.c -o bin_density.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c construct_dc.c -o construct_dc.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include/htslib/hts.h:35,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include/htslib/sam.h:31,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include/sam.h:28,
from parse_sam.h:4,
from construct_dc.c:23:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include/htslib/hts_log.h:72:1: warning: 'Rprintf' is an unrecognized format function type [-Wformat=]
HTS_FORMAT(printf, 3, 4);
^~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c parse_sam.c -o parse_sam.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sam.c -o sam.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c slice_dc.c -o slice_dc.o
slice_dc.c: In function 'slice_dc':
slice_dc.c:184:5: warning: 'slicep' may be used uninitialized in this function [-Wmaybe-uninitialized]
expand(slicep,new_vecp,rebuildc,wsize);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c visuals.c -o visuals.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o TransView.dll tmp.def R_init_TransView.o bam_plbuf.o bin_density.o construct_dc.o parse_sam.o sam.o slice_dc.o visuals.o C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/usrlib/i386/libhts.a -LC:/extsoft/lib/i386 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -lidn -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/TransView.buildbin-libdir/00LOCK-TransView/00new/TransView/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'TransView'
finding HTML links ... done
DensityContainer-class html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpM5bKH5/R.INSTALL13c81f255adc/TransView/man/DensityContainer-class.Rd:137: file link 'slice1-methods' in package 'TransView' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpM5bKH5/R.INSTALL13c81f255adc/TransView/man/DensityContainer-class.Rd:138: file link 'sliceN-methods' in package 'TransView' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpM5bKH5/R.INSTALL13c81f255adc/TransView/man/DensityContainer-class.Rd:140: file link 'rmTV-methods' in package 'TransView' does not exist and so has been treated as a topic
TVResults-class html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpM5bKH5/R.INSTALL13c81f255adc/TransView/man/TVResults-class.Rd:57: file link 'plotTVData-methods' in package 'TransView' does not exist and so has been treated as a topic
TransView-package html
annotatePeaks html
finding level-2 HTML links ... done
gtf2gr html
histogram-methods html
macs2gr html
meltPeak html
parseReads html
peak2tss html
plotTV html
plotTVData html
rmTV html
slice1 html
slice1T html
tvStats-methods html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'TransView' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c R_init_TransView.c -o R_init_TransView.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bam_plbuf.c -o bam_plbuf.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bin_density.c -o bin_density.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c construct_dc.c -o construct_dc.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include/htslib/hts.h:35,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include/htslib/sam.h:31,
from C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include/sam.h:28,
from parse_sam.h:4,
from construct_dc.c:23:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include/htslib/hts_log.h:72:1: warning: 'Rprintf' is an unrecognized format function type [-Wformat=]
HTS_FORMAT(printf, 3, 4);
^~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c parse_sam.c -o parse_sam.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sam.c -o sam.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c slice_dc.c -o slice_dc.o
slice_dc.c: In function 'slice_dc':
slice_dc.c:184:5: warning: 'slicep' may be used uninitialized in this function [-Wmaybe-uninitialized]
expand(slicep,new_vecp,rebuildc,wsize);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c visuals.c -o visuals.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o TransView.dll tmp.def R_init_TransView.o bam_plbuf.o bin_density.o construct_dc.o parse_sam.o sam.o slice_dc.o visuals.o C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/TransView.buildbin-libdir/TransView/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TransView' as TransView_1.32.0.zip
* DONE (TransView)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'TransView' successfully unpacked and MD5 sums checked